compute corrected Evalue for proteins

src/core/proteinmatch.cpp

@@ -83,7 +83,8 @@ void ProteinMatch::setEvalue(pappso::pappso_double evalue) {
 }
 
 pappso::pappso_double ProteinMatch::getEvalue() const {
-    return _evalue;
+    pappso::MsRunIdSp sp_msrun_id;
+    return getEvalue(sp_msrun_id);
 }
 void ProteinMatch::setProteinXtpSp(ProteinXtpSp protein_sp) {
     _protein_sp = protein_sp;
@@ -181,6 +182,45 @@ unsigned int ProteinMatch::countValidAndCheckedPeptideMassCharge(const pappso::M
     return sequence_list.size();
 }
 
+pappso::pappso_double ProteinMatch::getEvalue(const pappso::MsRunIdSp & sp_msrun_id) const {
+    std::map<QString, pappso::pappso_double> map_sequence_evalue;
+    for (auto & p_peptide_match : _peptide_match_list) {
+        if (p_peptide_match->isValidAndChecked()) {
+            QString sequence(p_peptide_match->getPeptideXtpSp().get()->getSequence());
+            pappso::pappso_double evalue = p_peptide_match->getEvalue();
+            if(sp_msrun_id.get() != nullptr) {
+                //within sample
+                if (p_peptide_match->getMsRunIdSp().get() == sp_msrun_id.get()) {
+                    auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
+                    if (ret.second == false) {
+                        if (ret.first->second < evalue) {//get best evalue for sequence
+                            ret.first->second = evalue;
+                        }
+                    }
+                }
+            }
+            else {
+                //overall samples
+                auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
+                if (ret.second == false) {
+                    if (ret.first->second < evalue) {//get best evalue for sequence
+                        ret.first->second = evalue;
+                    }
+                }
+            }
+        }
+    }
+
+    pappso::pappso_double evalue_prot = 1;
+    for (auto && peptide_pair: map_sequence_evalue) {
+        //evalue_prot += std::log10(peptide_pair.second);
+        evalue_prot *= peptide_pair.second;
+    }
+
+    //return (std::pow ((double) 10.0,evalue_prot));
+    return (evalue_prot);
+
+}
 
 pappso::pappso_double ProteinMatch::getPAI() const {
     pappso::MsRunIdSp sp_msrun_id;

src/core/proteinmatch.h

@@ -37,26 +37,37 @@ class IdentificationGroup;
 
 class ProteinMatch
 {
-  friend IdentificationGroup;
+    friend IdentificationGroup;
 public:
     ProteinMatch();
     ~ProteinMatch();
 
     const ProteinXtpSp & getProteinXtpSp() const;
     void setEvalue(pappso::pappso_double evalue);
+
+    /** @brief compute protein Evalue overall samples
+      * */
     pappso::pappso_double getEvalue() const;
-    pappso::pappso_double getCoverage() const;
     
-   /** @brief compute Protein Abundance Index (PAI)
-     * overall sample PAI computation (Rappsilber et al. 2002)
-     * */
+    /** @brief compute protein Evalue within samples
+      * */
+    pappso::pappso_double getEvalue(const pappso::MsRunIdSp & sp_msrun_id) const;
+
+
+    /** @brief protein coverage overall samples
+      * */
+    pappso::pappso_double getCoverage() const;
+
+    /** @brief compute Protein Abundance Index (PAI)
+      * overall sample PAI computation (Rappsilber et al. 2002)
+      * */
     pappso::pappso_double getPAI() const;
 
     /** @brief compute Protein Abundance Index (PAI) within sample
      * PAI computation (Rappsilber et al. 2002)
      * */
     pappso::pappso_double getPAI(const pappso::MsRunIdSp & sp_msrun_id) const;
-    
+
     void setProteinXtpSp(ProteinXtpSp protein_sp);
     void addPeptideMatch(PeptideMatch * peptide_match);
     std::vector<PeptideMatch *> & getPeptideMatchList();
@@ -81,17 +92,20 @@ public:
 
     const pappso::GrpProteinSp & getGrpProteinSp() const;
     const GroupingGroupSp & getGroupingGroupSp() const;
-    
+
 protected :
- 
+
     /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
     * */
     void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
 
     void setGroupingExperiment(GroupingExperiment * p_grp_experiment);
- 
+
     void setGroupInstance(GroupStore & group_store);
 
+private :
+    unsigned int countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const;
+
 private:
     pappso::GrpProteinSp _sp_grp_protein;
     GroupingGroupSp _sp_group;
@@ -106,7 +120,6 @@ private:
     /** @brief automatic filter result (false by default)
      */
     bool _proxy_valid = false;
-    unsigned int countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const;
 
 };